Hoot is the first novel for young readers by bestselling author Carl Hiaasen. In Hoot, Roy Eberhardt is the new kid in school and as such he is the current target of school bully, Dana Matherson. While under attack on the school bus by Dana, Roy sees a barefoot boy running away from the bus stop. Roy becomes fascinated with this boy, determined to find out who he is. Roy has no way of knowing that befriending this running boy will set him on a course that will end with a demonstration against one of the country's largest pancake houses. Hoot is a story of childhood that includes Hiaasen's trademark wit and takes a whole new group of readers on a ride through Hiaasen's Florida.

Roy Eberhardt is on the school bus when Dana Matherson, the school bully, forces his face against the window. While forced to look out, Roy sees a barefoot boy running away from the bus stop. Roy tries to find out who the boy is later at school, but no one seems to know anything about him. A few days later, Roy sees the boy again and starts to chase him, but Dana strikes again, choking Roy. Roy punches Dana and chases after the boy. However, before Roy catches up with the running boy, he is hit with a golf ball.

Back at school, Roy runs into a red haired girl who wants to know why Roy was leaving the bus that morning. Roy tries to explain himself, but the girl is tough and angry. The girl tells Roy to back off of his quest to uncover the identity of the running boy. However, Roy's curiosity is inspired and he decides to search for the boy anyway. Roy finds his camp beside the golf course, but the boy covers his head with a bag and leads him back out, not allowing Roy to see his face. The next day, the boy is gone.

The red haired girl, whom Roy now knows is Beatrice Leep, steals his bike and forces Roy to accompany her to a salvage yard. There, Beatrice tells Roy that the running boy is her stepbrother, Mullet Fingers. Mullet Fingers has run away from home and does not want anyone to know where he is because he believes his mother will have him sent to juvenile hall if she learns where he is. Roy promises to back off.

A few days later, Beatrice saves Roy from Dana and in return she asks his help with Mullet Fingers. It turns out that Mullet Fingers has gotten bitten by several dogs while vandalizing a construction site. The construction site is for a new Mother Paula's All American Pancake House, but there are burrowing owls on the property. Mullet Fingers has tried to stop the construction through letters to the corporation, but received a form letter in reply. Mullet Fingers is now trying to stop construction by repeatedly pulling out their survey stakes and vandalizing their equipment. This time, however, Mullet Fingers has gotten an infection from multiple dog bites.

Roy and Beatrice take Mullet Fingers to the hospital and Roy gives the hospital his own name as Mullet Fingers. This causes the hospital to call Roy's parents. When Roy overhears his parents arguing with hospital staff, he reveals the truth. However, Roy cannot tell them Mullet Fingers' real name, therefore protecting Mullet Fingers from discovery.

The corporation building the new restaurant becomes frustrated with the delays and decides to have the ground breaking ceremony that week despite the repeated vandalism. However, Roy and Beatrice manage to convince a large number of their friends and classmates to appear at the ceremony. Mullet Fingers too appears, buried in one of the owl's burrows. The students protest the danger to the owls and force the site to shut down once more. In the aftermath, it is revealed to the press that the corporation does not have the proper paperwork for building over the owl burrows. The corporation blames the whole ordeal on a hotheaded vice-president and decides to turn the site into a conservatory for the owls.